The text "variantchecker" will only be there in that file if a variant has an error in it. Thank you .
---------- Post updated at 03:39 PM ---------- Previous update was at 02:25 PM ----------
I added a warning to the menu:
If the user says "N" then it goes to the warning function and the variant is inputted again and the process continues as before. When the warning function is called I am trying to do post 3 (old variant removed and replaced with new variant). Thank you .
Code:
check() {
printf "\n\n"
awk 'NR>1 { if ($2 ~ /^\(/ ) {$1=""; print "Found error: ", $0} else { sub(/.*:/, "", $1); sub(/.*:/, "", $7); print "No error: " $1 "," $7}}' C:/Users/cmccabe/Desktop/Python27/${id}_name.txt
printf "Is the variant correct? Y/N "; read match_choice
case "$match_choice" in
[yY]) id="${id}"; position ;;
[nN]) awk 'FNR>1 FNR==NR {a[$i]; next}; !($1 in a)' ${id}_name.txt ${id}.txt; warning ;;
esac
}
warning() {
printf "\n\n"
printf "Please re-enter variant(s): "; IFS="," read -a variants
[ -z "$id" ] && printf "\n No ID supplied. Leaving match function." && sleep 2 && return
[ "$id" = "end" ] && printf "\n Leaving match function." && sleep 2 && return
for ((i=0; i<${#variants[@]}; i++))
do printf "NM_004004.5:%s\n" ${variants[$i]} >> c:/Users/cmccabe/Desktop/Python27/$id.txt
done
gjb2name
}
---------- Post updated 03-21-15 at 09:55 AM ---------- Previous update was 03-20-15 at 03:39 PM ----------
I made an edit to the awk that is underlined but I dont think its correct. Thank you .
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LEARN ABOUT OSX
script
SCRIPT(1) BSD General Commands Manual SCRIPT(1)NAME
script -- make typescript of terminal session
SYNOPSIS
script [-akq] [-t time] [file [command ...]]
DESCRIPTION
The script utility makes a typescript of everything printed on your terminal. It is useful for students who need a hardcopy record of an
interactive session as proof of an assignment, as the typescript file can be printed out later with lpr(1).
If the argument file is given, script saves all dialogue in file. If no file name is given, the typescript is saved in the file typescript.
If the argument command is given, script will run the specified command with an optional argument vector instead of an interactive shell.
The following options are available:
-a Append the output to file or typescript, retaining the prior contents.
-k Log keys sent to program as well as output.
-q Run in quiet mode, omit the start and stop status messages.
-t time
Specify time interval between flushing script output file. A value of 0 causes script to flush for every character I/O event. The
default interval is 30 seconds.
The script ends when the forked shell (or command) exits (a control-D to exit the Bourne shell (sh(1)), and exit, logout or control-D (if
ignoreeof is not set) for the C-shell, csh(1)).
Certain interactive commands, such as vi(1), create garbage in the typescript file. The script utility works best with commands that do not
manipulate the screen. The results are meant to emulate a hardcopy terminal, not an addressable one.
ENVIRONMENT
The following environment variable is utilized by script:
SHELL If the variable SHELL exists, the shell forked by script will be that shell. If SHELL is not set, the Bourne shell is assumed. (Most
shells set this variable automatically).
SEE ALSO csh(1) (for the history mechanism).
HISTORY
The script command appeared in 3.0BSD.
BUGS
The script utility places everything in the log file, including linefeeds and backspaces. This is not what the naive user expects.
It is not possible to specify a command without also naming the script file because of argument parsing compatibility issues.
When running in -k mode, echo cancelling is far from ideal. The slave terminal mode is checked for ECHO mode to check when to avoid manual
echo logging. This does not work when in a raw mode where the program being run is doing manual echo.
BSD January 22, 2004 BSD
03-21-2015
.